Oqani et. al. 2025: Star Alignment > AnnData Preprocessing & Embedding

Environment Setup (230707)

Install software from pip, apt, and Github. Load modules, configure workspace settings.

Download Star Count Matrices

Clean up the library directory names:

cd /content/wynton/group/wagner/NIMBUS/FASTQ/230705_NovaSeq_PR/
mv maltepee-FB1 FB1
mv maltepee-FB2 FB2
mv maltepee-FB3 FB3
mv maltepee-IVF1 IVF1
mv maltepee-IVF2 IVF2
mv maltepee-IVF3 IVF3
cd /content/

Load into AnnData

Perform Quality Filtering

Perform Cell Barcode Filtering

Uses a weighted histogram, rather than a cumulative histogram, to estimate the lower bound transcripts (UMIs) per barcode threshold.

Perform Mitochondrial Filtering

Perform Cell Doublet Filtering

Merge Libraries

Save Quality-Filtered Raw Counts h5ad

Load AnnData

Quick QC plots

Process and Normalize

Compute Embeddings and Perform Clustering

Plot Embeddings

Rank Genes Groups across Leiden clusters

Save Processed h5ad to Wynton